Reaction Boost (targeted MD): bond-making and breaking


Fig. 33 H₂O + propene → 1-propanol → H₂O + propene → 2-propanol


This tutorial requires AMS2024 or later.

The reaction boost (targeted MD) feature can be used to gradually transform one system into another during molecular dynamics.

This feature can be used, for example, to

In this tutorial we will set the reaction boost method to Pair, which means that the method will see which bonds need to break and form to go from reactant to product, and apply moving restraints on those bonds to gradually break and form them.

This can push the simulation over the (possibly large) reaction barriers.

The reaction boost method cannot generally be used to discover the “correct” or lowest-barrier reaction mechanism. For discovering new reaction mechanisms, see the PES Exploration and ACE Reaction tutorials.

If the applied restraints are mild enough then the path from reactant to product may be close to the minimum energy path. However, there is no guarantee that this is the case. To closer sample the minimum energy path, see the Nudged Elastic Band (NEB) tutorial.


The reaction boost method is quite different from the similarly named bond boost method.

In bond boost, if specific local motifs are identified during the simulation then restraints are added. When applying this method, you do not know what the end product will look like and the goal is to get the final structure.

In reaction boost (this tutorial), the restraints are essentially defined through the input structures. When applying this method, you already know what the end product will look like and the goal is to get intermediate structures.

Set up the calculation

Open AMSinput
File → Open →

You can also find this file in $AMSHOME/examples/MD_ReactionBoost.

You will get a warning to double-check your input, since importing .run files into AMSinput is not 100% reliable. We will go through all the input in more detail below.


If you manually set up your own systems, the order of the atoms must be same for all structures, similar to setting up NEB or PES Exploration calculations.

The easiest way to ensure this is to

  • import/draw the initial structure

  • Select → Select all

  • Edit → Copy

  • Edit → New Molecule

  • Edit → Paste

  • Manually move the atoms to form the target structure

Engine settings

The example loads the ReaxFF engine using the CHO.ff force field.

Feel free to modify the engine settings, especially if you do not have a ReaxFF license.

If you change the engine, you may need to set Task to Molecular Dynamics again.

Further down below we will change the engine to the MLPotential AIMNet2-wB97MD3 in order to also visualize uncertainties in the calculated energies during the trajectory.

Input systems

At the bottom of the 3D area, click the downward pointing arrow and select Multi View 2x2 Synced.

This shows all four input structures:


There are four input structures:

  • Mol-1: H₂O + propene

  • state2: 1-propanol

  • state3: H₂O + propene (identical to Mol-1)

  • state4: 2-propanol

The reaction boost method will transform the Mol-1 (H₂O+propene) system first into 1-propanol, then back to H₂O + propene, and finally into 2-propanol.


In this tutorial we do multiple transformations in a single simulation. However, this can lead to problems if one of the transformations is not successful.

Often, it is more reliable to just do a single transformation (to have two input structures instead of four) for Reaction Boost simulations.

At the bottom of the 3D area, click the downward pointing arrow and select Single view.

Molecular dynamics settings

On the main panel, click the MoreBtn button next to Task: Molecular Dynamics

Here you see that the number of steps is set to 3020, the time step to 0.5 fs, the sample frequency to 10 (save structure every 10 frames), and the initial temperature is 300 K.

Click the MoreBtn next to Thermostat

Here you see that there is a thermostat of type NHC with temperature 300 K, with a damping constant of 5.0 fs.


When using reaction boost, the temperature can rise significantly. Therefore the damping constant is set to a very small value of 5.0 fs in order to quickly cool down the system if it heats up.

For normal equilibration MD simulations you should never set the damping constant to such a small value!

To not sample too distorted structures, you may also consider setting the temperature to a lower value (for example, 100 K).

Reaction boost settings

In the Model menu, select MD… → Reaction Boost

Reaction boost has many input options. Below is an explanation of the most important ones.


Restraint type

When restraint type is set to Pair, it means that restraints are applied to make or break individual bonds.

These restraints thus act on internal coordinates, so it does not matter, for example, how the input structures are rotated relative to each other.

It does matter what the bond lengths are, since the restraints will be applied to match the bond length in the target structure. Therefore, it’s usually a good idea to preoptimize the structure using the same engine settings as during the MD.

For restraint type RMSD, see the other Reaction Boost tutorial.

Target systems

You can add or remove target systems by clicking the AddButton and DeleteButton buttons.

The order in which the target systems are visited during the MD is determined by the order in the panel on the right, not the order of the input systems in the 3D area on the left.

Make sure that all systems except one is listed in the target systems. The initial structure for the MD is the system not listed among the Target systems.

Here the Target systems are state2, state3, state4. This means that the initial structure will be Mol-1.

General reaction boost settings


See the reaction boost (targeted MD) AMS documentation for details about all of these input options.

When Move type is set to LogForce, like here, it means that the forces will gradually be increased. The magnitude of the force depends on both the MD step and how far away from the target structure the current structure is.

Initial fraction set to 0.1 means that the log force will be 10% of the final (maximum) value at the very first step.

Steps per target specifies how many MD steps to do for each target system. Here it is set to 1000. Since there are 3 target systems the reaction boost will be active for a total of 3000 MD steps. In the general MD panel, the number of steps was 3020. This means that the last 20 steps of the MD simulation are not affected by reaction boost but behave like a normal NVT simulation.

Reaction boost restraint types and settings

Non-bonded restraints (optional): These restraints make sure that no unwanted new bonds are formed during the MD. By setting Exponential, a repulsive potential is added between all atoms that are not bonded in the initial structure and not bonded in the target structure.

Bonded restraints (optional): These restraints make sure that bonds that are not intended to break do not break. By settings Harmonic, a harmonic potential keeps all atoms that are bonded in the initial structure and that are not supposed to break during the simulation intact.

Bond breaking restraints (recommended if at least 1 bond breaks): By setting Erf a bond-breaking force is added to the bonds that are supposed to break. In this case, the maximum applied force is 0.1 hartree/bohr.

Bond making restraints (recommended if at least 1 bond forms): By setting Erf a bond-making force is added to the bonds are supposed to form. In this case, the maximum applied force is 0.4 hartree/bohr.

There are also other restraint types. See the documentation for details.


If your intended transformation is not successful, you may consider increasing the bias by for example increasing the force constant, the max force, or number of steps.

Save and run the job

Save and run the job. If you use the ReaxFF engine it should only take a few seconds to finish.

Open the trajectory in AMSmovie to visualize the results. It should look something like this:


Visualize energy uncertainties with AIMNet2 ML Potential

The new AIMNet2 ML potential models in AMS2024 can calculate energy uncertainties that can be visualized during the MD simulation.

If you haven’t already, install/download the AIMNet2 models: SCM → Packages
Click the ML Options and select a suitable option
Select AIMNet2 and install

This will download and install the AIMNet2 models from the SCM servers. It may take a while to complete the installation.

Open AMSinput
File → Open →
Change from ReaxFFPanel to MLPotentialPanel
Set Task to Molecular Dynamics
Set Model to AIMNet2-wB97MD3
Save and run the job

The job will take a few minutes to finish

Select the job in AMSJobs
SCM → Movie

Note that the Energy shown includes the restraint energies and kinetic energy. Typically, it’s more useful to look at the “engine energy”, which is potential energy calculated by the engine (without restraints and kinetic energy).

Graph → Delete graph
Graph → Engine Energy

In this graph, you can see the calculated energy uncertainty as a shaded red region around the line. It is easier to see if you zoom in a bit.


You can also plot the uncertainty in its own graph:

Graph → Add graph
Graph → Other… → Engine Energy U

Here, you can clearly see that the energy uncertainty is higher when the molecules are separate.

The highest uncertainty is obtained during the transition into 1-propanol.